Objectives:

What is R, and why use it?

R is a free programming environment for data processing and statistical analysis. R allows you to write scripts that combine data files, clean data, and run analyses. R is really useful for conducting reproducible research (research that documents all of the steps between raw data and results in a way that can be verified), automating analytical steps, creating custom high-quality visualizations, and conducting a wide range of statistical analyses from basic t-tests to multivariate multilevel Bayesian regression.

This document details steps to get started in R as part of the R for researchers in Communication Sciences and Disorders workshop (August 2022). It synthesizes already-published materials for teaching R in a way that is tailored to this workshop. Anyone interested in the full materials can find them here: https://psyteachr.github.io/.

Installing R

note, more detailed instructions can be found here: https://rstudio-education.github.io/hopr/starting.html

Install base R. This installs the R programming language and a simple GUI (from here on, we will refer to it as the R GUI). Choose the download link for your operating system (Linux, Mac OS X, or Windows).

Download page for R and the R GUI

If you have a Mac, install the latest release from the newest R-x.x.x.pkg link (or a legacy version if you have an older operating system). After you install R, you should also install XQuartz to be able to use some visualisation packages.

If you are installing the Windows version, choose the “base” subdirectory and click on the download link at the top of the page. After you install R, you should also install RTools; use the “recommended” version highlighted near the top of the list.

If you are using Linux, choose your specific operating system and follow the installation instructions.

If you have trouble with installation, R can also be used online: RStudio Cloud is a free online service that allows access to R and RStudio.

A view of the R GUI on mac

A view of the R GUI on mac

Installing RStudio

RStudio is an “IDE” (Integrated Development Environment) for using R (and some other languages). RStudio allows us to run R code and comes with lots of other features that makes using R easier and more efficient.

Go to rstudio.com and download the RStudio Desktop (Open Source License) version for your operating system under the list titled Installers for Supported Platforms.

If you’re unsure about where something is in RStudio, try finding it in the cheat sheet here: https://raw.githubusercontent.com/rstudio/cheatsheets/main/rstudio-ide.pdf

The RStudio interface

The RStudio interface

There are a few settings you should fix immediately after updating RStudio. Go to Global Options... under the Tools menu (⌘,), and in the General tab, uncheck the box that says Restore .RData into workspace at startup. If you keep things around in your workspace, things will get messy, and unexpected things will happen. You should always start with a clear workspace. This also means that you never want to save your workspace when you exit, so set this to Never. The only thing you want to save are your scripts.

If you’re having trouble finding this setting, make a note to yourself and let us know when we get started on day 1

Installing Packages

“base R” (everything that comes with the initial installation of R) comes with many basic functions for data wrangling, plotting, and statistical analysis, but most people (including us, and this workshop) use additional packages that add additional features to R.

The main repository where packages reside is called CRAN, the Comprehensive R Archive Network. A package has to pass strict tests devised by the R core team to be allowed to be part of the CRAN archive. You can install from the CRAN archive with the install.packages() function. Try installing the following packages:

# installs the package tidyverse, which includes data wrangling and viz tools
install.packages("tidyverse")
# installs the package here, which helps with file management
install.packages("here")
# install the usethis package, which has lots of useful functions
install.packages("usethis")

Sometimes, installing packages can result in errors. If you run into an error, copy and paste the error into a sticky/note on your computer and save it for the beginning of the workshop.

Note: Never install packages within a script, only install scripts from the console

Installing LaTeX (optional)

You can install the LaTeX typesetting system to produce PDF reports from RStudio. To generate PDF reports, you will additionally need to install tinytex (Xie, 2022) package and run the following code:

install.packages("tinytex")
tinytex::install_tinytex()

Troubleshooting

Occasionally, you might have a few problem packages that don’t install or update cleanly. If you try to update a package and get an error message that says something like Warning in install.packages : installation of package ‘vctrs’ had non-zero exit status or perhaps Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘rlang’ 0.4.9 is being loaded, but >= 0.4.10 is required. One solution I have found is to manually uninstall the package, restart R, and then install the package new, rather than trying to update an existing version.

# Uninstall the problem package
remove.packages("package_name")

# Then restart R. Choose session from the top menu and then restart R

# Then install the package fresh
install.packages("package")